For the simulations during the optimization procedure, the convolution method is chosen as it is computationally efficient [1]}. This fast method works extremely well for the qualitative simulation of ADF images of very thin materials, but it has the major drawback that contrast reversals (e.g. negative phase at the center of the hexagons) as they appear in phase images cannot be reproduced as the convolution method always results in positive values. Nevertheless, it shows that the structural optimization indeed leads to a reliable match. This match is not expected to be perfect, as the difference image shows residual features rather than noise (see Supplementary Figure 1) but is still sufficient for a proper quantification of the chemical elements and assignment of the projected positions.
We also want to point out that under these low-dose conditions, the SSB image is more suitable for the refinement of the atomic positions than the ADF image as it has a significantly better signal-to-noise ratio. The extracted positions are adopted for the ADF image, where only the atomic scattering factors were included in the optimization process.
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